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The cyanobacterial cytochrome b 6 f complex is central for the coordination of photosynthetic and respiratory electron transport and also for the balance between linear and cyclic electron transport. The development of a purification strategy for a highly active dimeric b 6 f complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 enabled characterization of the structural and functional role of the small subunit PetP in this complex. Moreover, the efficient transformability of this strain allowed the generation of a DpetP mutant. Analysis on the whole-cell level by growth curves, photosystem II light saturation curves, and P700 + reduction kinetics indicate a strong decrease in the linear electron transport in the mutant strain versus the wild type, while the cyclic electron transport via photosystem I and cytochrome b 6 f is largely unaffected. This reduction in linear electron transport is accompanied by a strongly decreased stability and activity of the isolated DpetP complex in comparison with the dimeric wild-type complex, which binds two PetP subunits. The distinct behavior of linear and cyclic electron transport may suggest the presence of two distinguishable pools of cytochrome b 6 f complexes with different functions that might be correlated with supercomplex formation.

BackgroundProteogenomics combines the cutting-edge methods from genomics and proteomics. While it has become cheap to sequence whole genomes, the correct annotation of protein coding regions in the genome is still tedious and error prone. Mass spectrometry on the other hand relies on good characterizations of proteins derived from the genome, but can also be used to help improving the annotation of genomes or find species specific peptides. Additionally, proteomics is widely used to find evidence for differential expression of proteins under different conditions, e.g. growth conditions for bacteria. The concept of proteogenomics is not altogether new, in-house scripts are used by different labs and some special tools for eukaryotic and human analyses are available.ResultsThe Bacterial Proteogenomic Pipeline, which is completely written in Java, alleviates the conducting of proteogenomic analyses of bacteria. From a given genome sequence, a naïve six frame translation is performed and, if desired, a decoy database generated. This database is used to identify MS/MS spectra by common peptide identification algorithms. After combination of the search results and optional flagging for different experimental conditions, the results can be browsed and further inspected. In particular, for each peptide the number of identifications for each condition and the positions in the corresponding protein sequences are shown. Intermediate and final results can be exported into GFF3 format for visualization in common genome browsers.ConclusionsTo facilitate proteogenomics analyses the Bacterial Proteogenomic Pipeline is a set of comprehensive tools running on common desktop computers, written in Java and thus platform independent. The pipeline allows integrating peptide identifications from various algorithms and emphasizes the visualization of spectral counts from different experimental conditions.

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